Two new sub-variants have been detected from the new Alpha variant sub-lineages including one with two additional mutations G204P and K68stop were detected on nucleoprotein and ORF8 respectively.
Alarmingly the other sub-variant had two additional spike mutations D138Y and A701V of which the D138Y mutation is the signature mutation found in the Beta variant while the A701V mutation is one of the signature mutations of the Gamma variant!
The new Alpha sub-variants are suspected to be causing the new surges in parts of Europe including Germany, Austria, Slovenia, Czech Republic, Slovakia, Poland, Romania, Denmark and even Ukraine besides the various Delta-sub-variants.
Even more worrisome is the possibility of recombinant events involving the alpha and delta sub-variants in Europe.
The study findings were published on a preprint server and are currently being peer reviewed.
SARS-CoV-2 evolution plays a significant role in shaping the dynamics of the COVD-19 pandemic.
To monitor the evolution of SARS-CoV-2 variants, through international collaborations, we performed genomic epidemiology analyses on a weekly basis with SARS-CoV-2 samples collected from a border region between Germany, Poland and the Czech Republic in a global background.
For identified virus mutant variants, active viruses were isolated and functional evaluations were performed to test their replication fitness and neutralization sensitivity against vaccine elicited serum neutralizing antibodies. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. Of note, this B.1.1.7 sub-lineage is the predominant B.1.1.7 variant in several European countries, such as Czech Republic, Austria and Slovakia.
The earliest samples belonging to this sub-lineage were detected in November 2020 in a few countries in the European continent, but not in the UK. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Beta and Gamma variants, respectively.
Antibody neutralization assay of virus variant isolations has revealed that the variant with extra spike mutations is 3.2-fold less sensitive to vaccine-elicited antibodies as compared to other B.1.1.7 variants tested, indicating potential for immune evasion, but it also exhibited reduced replication fitness.
The wide spread of this B.1.1.7 sub-lineage was related to the pandemic waves in early 2021 in various European countries. These findings about the emergence, spread, evolution, infection and transmission abilities of this B.1.1.7 sub-lineage add to our understanding about the pandemic development in Europe, and could possibly help to prevent similar scenarios in future.